It's probably too long a period of time since there was any response to your post, but I thought I would give it a try. According to the previous forum post you are referencing, the selection of the "smallest atoms possible" is referring to the interface builder window with all calculated in-plane strains depending on whether the first layer, second layer, or both layers are strained. You want to select the dot on the lower panel that gives the lowest number of atoms while still minimizing the amount of in-plane strain resulting between the first and second layers.
The "repeat a bit on both sides of the interface" part would mean to add additional atomic layers to both sides of the interface using the "+" buttons you see under each displayed bulk material within the interface builder pulldown menu. Additional layers for each bulk material that are joined together to form the interface will be included in the supercell slab model. There are other ways to add more layers to both sides of the interface, but I will leave that out of the discussion for now. I hope that helps some.
